SMTL ID : 6pzw.1

CryoEM derived model of NA-22 Fab in complex with N9 Shanghai2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.106, W.398 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain D: N.106, W.398 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain I: N.106, W.398 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain J: N.106, W.398 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:W.398

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2: 19 residues within 4Å: Chain A: N.160, N.161 Chain B: S.27, S.95 Chain D: R.288, N.290, D.291, R.324, I.326, T.328, E.335, K.349, I.351, Q.352, G.353, F.413, L.414, G.415, Q.416 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.413 Hydrogen bonds: D:G.353, D:G.353 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.4: 19 residues within 4Å: Chain D: N.160, N.161 Chain E: S.27, S.95 Chain I: R.288, N.290, D.291, R.324, I.326, T.328, E.335, K.349, I.351, Q.352, G.353, F.413, L.414, G.415, Q.416 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:F.413 Hydrogen bonds: I:G.353, I:G.353 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6: 19 residues within 4Å: Chain G: S.27, S.95 Chain I: N.160, N.161 Chain J: R.288, N.290, D.291, R.324, I.326, T.328, E.335, K.349, I.351, Q.352, G.353, F.413, L.414, G.415, Q.416 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:F.413 Hydrogen bonds: J:G.353, J:G.353 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.7: 19 residues within 4Å: Chain A: R.288, N.290, D.291, R.324, I.326, T.328, E.335, K.349, I.351, Q.352, G.353, F.413, L.414, G.415, Q.416 Chain J: N.160, N.161 Chain K: S.27, S.95 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.413 Hydrogen bonds: A:G.353, A:G.353

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 4 residues within 4Å: Chain D: N.43, F.44, N.46, N.195 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.43 Hydrogen bonds: D:N.195 NAG.10: 4 residues within 4Å: Chain I: N.43, F.44, N.46, N.195 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:N.43 Hydrogen bonds: I:N.195 NAG.11: 4 residues within 4Å: Chain J: N.43, F.44, N.46, N.195 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:N.43 Hydrogen bonds: J:N.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X. et al., Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies. Cell Host Microbe (2019)

Release Date

2019-12-04

Peptides

Neuraminidase: ADIJ
NA-22 fragment antigen binding light chain: BEGK
NA-22 fragment antigen binding heavy chain: CFHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

I
C

J
B

B
I

E
E

G
G

K
L

C
K

F
F

H
J

L
H

Neuraminidase

NA-22 fragment antigen binding light chain

NA-22 fragment antigen binding heavy chain

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